DESCRIPTION
r.pi (raster patch index) provides various functions to analyse
spatial attributes of a landscape. It has a focus on patch-based indices
but delivers class-based indices as well. r.le and its successor
r.li provide landscape indices.
A list with a short description of the r.pi modules can be found
below. More in depth description of a certain module (commands, flags,
options) can be found in the respective folder (like
r.pi.graph). The functions/algorithms
of the modules are not yet very extensive but will be expanded in the
future. Please submit any bug/feature you might encounter to improve the
functionality.
The program will interactively query the user for input, output and
options (GUI). However the module can be also run from the terminal
prompt (CLI) and might be implemented in e.g. a bash-script.
It is highly recommended to read the help pages or e.g the overview
documents of
Fragstats
to get a better impression of problems, possibilities and caveats.
OVERVIEW
r.pi.rectangle - Performs statistical analysis on values of patches from the given raster map.
r.pi.corrwindow - Calculates correlation of two raster maps by calculating correlation function of two corresponding rectangular areas for each raster point and writing the result into a new raster map.
r.pi.energy - Individual-based dispersal model for connectivity analysis - energy based.
r.pi.energy.iter - Individual-based dispersal model for connectivity analysis (energy based) using iterative patch removal.
r.pi.fragment.dist - Calculates correlation of two raster maps by calculating correlation function of two corresponding rectangular areas for each raster point and writing the result into a new raster map.
r.pi.enn - Determines patches of given value and performs a nearest-neighbor analysis.
r.pi.index - Computation of fragmentation indices.
r.pi.enn.iter - Patch relevance for Euclidean Nearest Neighbor patches.
r.pi.neigh - Neighbourhood analysis - value of patches within a defined range.
r.pi.enn - Analysis of n-th Euclidean Nearest Neighbor distance.
r.pi.nlm - Creates a random generated map with values 0 or 1by given landcover and fragment count.
r.pi.nlm.circ - Creates a random landscape with defined attributes.
r.pi.nlm.stats - Neutral Landscape Generator - index statistics
r.pi.corearea - Variable edge effects and core area analysis
r.pi.corrwin - Moving window correlation analysis.
r.pi.csr.mw - Complete Spatial Randomness analysis on moving window.
r.pi.export - Export of patch based information.
r.pi.graph - Graph Theory for connectivity analysis.
r.pi.graph.iter - Graph Theory - iterative removal (patch relevance analysis).
r.pi.graph.red - Graph Theory - decreasing distance threshold option.
r.pi.grow - Size and suitability based region growing.
r.pi.import - Import and generation of patch raster data
r.pi.index - Basic patch based indices
r.pi.lm - Linear regression analysis for patches.
r.pi.prob.mw - Probability analysis of 2 random points being in the same patch.
r.pi.rectangle - Generates a rectangle based on a corner coordinate.
r.pi.searchtime - Individual-based dispersal model for connectivity analysis (time-based)
r.pi.searchtime.iter - Individual-based dispersal model for connectivity analysis (time-based) using iterative removal of patches
r.pi.searchtime.mw - Individual-based dispersal model for connectivity analysis (time-based) using moving window
TODO: update below with above...
General and Connectivity Indices
- r.pi.index: Calculations of basic indices (area, SHAPE etc.)
- r.pi.enn: Area, SHAPE and distance to n-th Euclidean Nearest Neighbor
- r.pi.fnn: Area, SHAPE and distance to n-th Functional Nearest Neighbor
- r.pi.odc: Area and distance to omnidirectional n-th Nearest Neighbors
- r.pi.neigh: Extraction of values of patches in defined buffer region
- r.pi.prox: Calculation of Proximity and Modified Proximity Index for patches in buffer region
- r.pi.graph: Various connectivity indices within the Graph Theory
Individual-based dispersal models
Patch-Relevance
Neutral Landscape Model
- r.pi.nlm: Generation of a neutral landscape (fractal)
- r.pi.nlm.stats:Statistical analysis of landscapes based on permutation of neutral landscapes
- r.pi.nlm.circc:Generation of a neutral landscape (circular)
various modules
- r.pi.corearea:Calculation of core area based on costmatrix
- r.pi.prob.mw:Probability of two random points being in the same patch
- r.pi.rectangle: Generation of rectangles based on coordinate points
- r.pi.import:Import of values to corresponding patches
- r.pi.export:Export of values from patches
- r.pi.lm:Residuals of a Linear Regression between 2 rasters are provided as raster
- r.pi.corrwin:A correlation between the pixels of two raster
files inside a moving analysis is calculated
EXAMPLES
Calculation of the SHAPE-Index
Input can be generated by r.pi.nlm, for example:
# generate random landscape with 50% cover
r.pi.nlm output=NLM_in landcover=50 sharpness=0.5
# use the class 1 of the above generated landscape for computation of SHAPE-Index
r.pi.index input=NLM_in keyval=1 output=NLM_in.shape method=shape
Calculation of the distance to the first and 10th Nearest Neighbor
Input generated by r.pi.nlm, for example:
# generate random landscape with 50% cover
r.pi.nlm output=NLM_in landcover=50 sharpness=0.5
# first NN
r.pi.index input=NLM_in keyval=1 output=NLM_in.enn1 method=ENN
# 10th NN
r.pi.enn input=NLM_in output=NLM_in.enn10 method=distance number=10
# 1-10th NN
r.pi.enn input=NLM_in output=NLM_in.enn10 method=distance number=1-10
NOTE
The maximum number of patches that can be queried at one time depend on
the module and might also be influenced by the resolution.
SEE ALSO
r.buffer.rect,
r.corrwindow,
r.energy,
r.energy.iter,
r.fragment,
r.fragment.dist,
r.fragment.enn,
r.fragment.iter,
r.fragment.neighbors,
r.fragment.nn,
r.nlm,
r.nlm.fractal,
r.nlm.stats,
r.pi.corearea,
r.pi.corrwin,
r.pi.csr.mw,
r.pi.export,
r.pi.graph,
r.pi.graph.dec,
r.pi.graph.iter,
r.pi.graph.red,
r.pi.grow,
r.pi.import,
r.pi.index,
r.pi.lm,
r.pi.odc,
r.pi.prob.mw,
r.pi.rectangle,
r.searchtime,
r.searchtime.iter,
r.searchtime.mw
r.le,
r.li
REFERENCES
- Wegmann, M., Shirinova, E., Neteler, M., Rocchini, D., Schmidt, M.,
Dech, S.: r.pi: Semi-automatic spatial pattern analysis of remotely
sensed land cover data. Software review. Submitted.
Disclaimer
This software is released under the GPL license, hence also the limitation
of liability. This software was designed for a certain project and its research
questions. Its nomenclature might not be concordant with other software packages.
Moreover its capabilities are yet limited and can not be compared to such of e.g.
Fragstats, however every user is invited to extend, modify or fix the
functionality of r.pi as long as the new code comply with the GPL.
AUTHORS
Programming: Elshad Shirinov
Scientific concept: Martin Wegmann
Department of Remote Sensing
Remote Sensing and Biodiversity Unit
University of Wuerzburg, Germany
Last changed: $Date$